Gene Losses

Overview

Gene content shows considerable variation among eukaryotic genomes and the recent availability of many complete-genome sequences allowed us to consistently quantify gene losses in 5 insect and 5 vertebrate species.

Goals

- quantification of gene losses and mapping them to the species tree
- identification of functionally linked lost genes and, possibly, identification of lost or rearranged pathways
- measuring the constraints of the gene repertoire evolution

Methods

Groups of orthologous groups of the complete proteomes of 5 insect and 5 vertebrate species were automatically identified using a variant of a strategy used previously (on the basis of all-against-all protein Smith-Waterman comparisons, followed by merging of reciprocally best matching triangles between each set of three species and addition of inparalogs, genes that are more similar within the genome than to any other protein in the other genomes).
Mapping of the losses to the tree was done assuming parsimony by minimizing the total number of losses over the phylogenetic tree.

Results

We identified known gene losses that confirmed our approach as well as hundreds of new gene losses in each lineage. Insects lost 2-3x more ancient genes than vertebrates. Interestingly, the number of losses per branch correlates with evolutionary rate and divergence time. We are studying some selected coordinated losses in more detail.
Quantification of orthologous gene losses in insects and vertebrates.

Quantification of ortholog losses in insects and vertebrates

The increasing number of sequenced insect and vertebrate genomes of variable divergence enables refined comparative analyses to quantify the major modes of animal genome evolution and allows tracing of gene genealogy (orthology) and pinpointing of gene extinctions (losses), which can reveal lineage-specific traits.

Results

We compared the gene repertoires of 5 vertebrates and 5 insects, including honeybee and Tribolium beetle that represent insect orders outside the previously sequenced Diptera, to consistently quantify losses of orthologous groups of genes. We found hundreds of lost Urbilateria genes in each of the lineages and assessed their phylogenetic origin. The rate of losses correlates well with the species' rates of molecular evolution and radiation times, without distinction between insects and vertebrates, indicating their stochastic nature. Remarkably, this extends to the universal single-copy orthologs, losses of dozens of which have been tolerated in each species. Nevertheless, the propensity for loss differs substantially among genes, where roughly 20% of the orthologs have an 8-fold higher chance of becoming extinct. Extrapolation of our data also suggests that the Urbilateria genome contained more than 7,000 genes.

Conclusions

Our results indicate that the seemingly higher number of observed gene losses in insects can be explained by their 2-3 fold higher evolutionary rate. Despite the profound effect of many losses on cellular machinery, overall, they seem to be guided by neutral evolution.